It seems, directories or files starting with a dot are not published as well.

So the solution was quite simple: in the shell script I use for publishing the site I added a line which will touch a file called .nojekyll as suggested in the help article before invoking the maven-scm-publish-plugin and it worked :-)

Update: I had written an email to github before I just tried the .nojekyll solution and received an answer quite promptly, jekyll/site.rb has more explanations.

Update 2: instead of touching .nojekyll you may add src/site/resources/.nojekyll in your project as outlined in Adding Extra Resources of the maven-site-plugin documentation.